Identification of Differentially Expressed Genes and Pathways Involved in Growth and Development of Mesona chinensis Benth Under Red- and Blue-Light Conditions

Mesona chinensis Benth (MCB) is an important Chinese herbal medicine. The plant factories might be one of the ways to solve the shortage of MCB supply. In this study, the MCB seedlings were treated under the red (R) and blue (B) lights in the plant factory. Results showed that the red light promoted the growth and development of MCB in comparison with the blue light. Under the red-light condition, the biomass, plant height, and root characteristics were significantly higher than those under blue-light condition, while the soil and plant analyzer development (SPAD) under the red-light treatment was significantly lower than that under the blue-light treatment. Red light also significantly promoted the content of soluble sugar and pectin of MCB compared with blue light. Transcriptome analysis showed that a total of 4,165 differentially expressed genes (DEGs) were detected including 2,034 upregulated and 2,131 downregulated. Of these, 1,112 DEGs including 410 upregulated and 702 downregulated genes were associated with 111 pathways. Moreover, a total of 8,723 differentially expressed transcription factors (TFs) were identified in R vs. B, and these TFs were distributed in 56 gene families. Metabonomic results revealed that a total of 184 metabolites and 99 differentially expressed metabolites (DEMs) (42 upregulated and 57 downregulated) were identified in the red- and blue-light treatments. Integrative analysis of transcriptome and metabolome unveiled that a total of 24 pathways included 70 compounds (metabolites) and were associated with 28 unigenes. In particular, these pathways included starch and sucrose metabolism, phenylpropanoid biosynthesis, cysteine and methionine metabolism, glycolysis/gluconeogenesis, and pentose and glucuronate interconversions. The unigenes included asparagine synthetase (AS), thymidine kinase (TK), alpha, alpha-trehalose-phosphate synthase (TPS), phosphatase IMPL1 (IMPL1), dihydroflavonol 4-reductase (D4R), and 4-coumarate-CoA ligase-like 6 (4CL6), bifunctional aspartokinase-homoserine dehydrogenase 1 (thrA), and abscisic acid 8′-hydroxylase 2 isoform X1 (ABA8). It was indicated that these pathways and genes might play important roles in the growth and development of MCB. This study laid a foundation for the future research of MCB.

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Single Wavelengths of LED Light Supplement Promote the Biosynthesis of Major Cyclic Monoterpenes in Japanese Mint

Plants ◽

10.3390/plants10071420 ◽

2021 ◽

Vol 10 (7) ◽

pp. 1420

Author(s):

Takahiro Ueda ◽

Miki Murata ◽

Ken Yokawa

Keyword(s):

Blue Light ◽

Solid Phase ◽

Glandular Trichomes ◽

Red Light ◽

Glandular Trichome ◽

Pulse Amplitude ◽

Light Treatment ◽

Led Light ◽

Trichome Formation ◽

Japanese Mint

Environmental light conditions influence the biosynthesis of monoterpenes in the mint plant. Cyclic terpenes, such as menthol, menthone, pulegone, and menthofuran, are major odor components synthesized in mint leaves. However, it is unclear how light for cultivation affects the contents of these compounds. Artificial lighting using light-emitting diodes (LEDs) for plant cultivation has the advantage of preferential wavelength control. Here, we monitored monoterpene contents in hydroponically cultivated Japanese mint leaves under blue, red, or far-red wavelengths of LED light supplements. Volatile cyclic monoterpenes, pulegone, menthone, menthol, and menthofuran were quantified using the head-space solid phase microextraction method. As a result, all light wavelengths promoted the biosynthesis of the compounds. Remarkably, two weeks of blue-light supplement increased all compounds: pulegone (362% increase compared to the control), menthofuran (285%), menthone (223%), and menthol (389%). Red light slightly promoted pulegone (256%), menthofuran (178%), and menthol (197%). Interestingly, the accumulation of menthone (229%) or menthofuran (339%) was observed with far-red light treatment. The quantification of glandular trichomes density revealed that no increase under light supplement was confirmed. Blue light treatment even suppressed the glandular trichome formation. No promotion of photosynthesis was observed by pulse-amplitude-modulation (PAM) fluorometry. The present result indicates that light supplements directly promoted the biosynthetic pathways of cyclic monoterpenes.

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Transcriptome Analysis of Differentially Expressed mRNA Related to Pigeon Muscle Development

Animals ◽

10.3390/ani11082311 ◽

2021 ◽

Vol 11 (8) ◽

pp. 2311

Author(s):

Hao Ding ◽

Yueyue Lin ◽

Tao Zhang ◽

Lan Chen ◽

Genxi Zhang ◽

...

Keyword(s):

Gene Expression ◽

Skeletal Muscle ◽

Differentially Expressed Genes ◽

Growth And Development ◽

Muscle Development ◽

Expression Patterns ◽

Differentially Expressed ◽

Pathway Enrichment Analysis ◽

Growth Stages ◽

Gene Expression And Regulation

The mechanisms behind the gene expression and regulation that modulate the development and growth of pigeon skeletal muscle remain largely unknown. In this study, we performed gene expression analysis on skeletal muscle samples at different developmental and growth stages using RNA sequencing (RNA−Seq). The differentially expressed genes (DEGs) were identified using edgeR software. Weighted gene co−expression network analysis (WGCNA) was used to identify the gene modules related to the growth and development of pigeon skeletal muscle based on DEGs. A total of 11,311 DEGs were identified. WGCNA aggregated 11,311 DEGs into 12 modules. Black and brown modules were significantly correlated with the 1st and 10th day of skeletal muscle growth, while turquoise and cyan modules were significantly correlated with the 8th and 13th days of skeletal muscle embryonic development. Four mRNA−mRNA regulatory networks corresponding to the four significant modules were constructed and visualised using Cytoscape software. Twenty candidate mRNAs were identified based on their connectivity degrees in the networks, including Abca8b, TCONS−00004461, VWF, OGDH, TGIF1, DKK3, Gfpt1 and RFC5, etc. A KEGG pathway enrichment analysis showed that many pathways were related to the growth and development of pigeon skeletal muscle, including PI3K/AKT/mTOR, AMPK, FAK, and thyroid hormone pathways. Five differentially expressed genes (LAST2, MYPN, DKK3, B4GALT6 and OGDH) in the network were selected, and their expression patterns were quantified by qRT−PCR. The results were consistent with our sequencing results. These findings could enhance our understanding of the gene expression and regulation in the development and growth of pigeon muscle.

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Identification and expression of the trehalose-6-phosphate synthase gene family members in tomato exposed to different light spectra

Archives of Biological Sciences ◽

10.2298/abs160325082c ◽

2017 ◽

Vol 69 (1) ◽

pp. 93-101

Author(s):

Zexiong Chen ◽

Juan Lou

Keyword(s):

Plant Growth ◽

Blue Light ◽

White Light ◽

Growth And Development ◽

Light Quality ◽

Red Light ◽

Floral Transition ◽

Stem Length ◽

Pcr Analysis ◽

Phosphate Synthase

Light is the source of energy for plants. Light wavelengths, densities and irradiation periods act as signals directing morphological and physiological characteristics during plant growth and development. To evaluate the effects of light wavelengths on tomato growth and development, Solanum lycopersicum (cv. micro-Tom) seedlings were exposed to different light-quality environments, including white light and red light supplemented with blue light (at ratios of 3:1 and 8;1, respectively). Tomatoes grown under red light supplemented with blue light displayed significantly shorter stem length, a higher number of flower buds and rate of fruit set, but an extremely late flowering compared to white-light-grown plants. To illustrate the mechanism underlying the inhibition of stem growth and floral transition mediated by red/blue light, 10 trehalose-6-phosphate synthase (TPS) genes were identified in tomato, and bioinformatics analysis was performed. qRT-PCR analysis showed that SlTPSs were expressed widely throughout plant development and SlTPS1 was expressed at extremely high levels in stems and buds. Further analysis of several flowering-associated genes and microRNAs showed that the expressions of SlTPS1, SlFT and miR172 were significantly downregulated in tomato grown under red and blue light compared with those grown under white light, whereas miR156 transcript levels were increased. A regulatory model underlying vegetative growth and floral transition regulated by light qualities is presented. Our data provide evidence that light quality strongly affects plant growth and phase transition, most likely via the TPS1-T6P signaling pathway.

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Germination responses of seeds of Desmodium triflorum

International Journal of Scientific Reports ◽

10.18203/issn.2454-2156.intjscirep20180392 ◽

2018 ◽

Vol 4 (2) ◽

pp. 19 ◽

Cited By ~ 1

Author(s):

Niroj Paudel ◽

Prakash Deep Rai

Keyword(s):

Seed Germination ◽

Blue Light ◽

White Light ◽

Red Light ◽

Light Condition ◽

Dark Condition ◽

Percentage Germination ◽

Negative Effect

Background: Germination of Desmodium triflorum is used for the scarification using the acid is valuable for the different light condition.Methods: The sample was collected as four month of interval of time and the seed is treated with acids with different time. Results: seeds scarified with sulfuric acids for 10 min before sowing had better germination than those scarified for 5 and 15 min. Among them light qualities, red and white light had slightly promoted effect whereas blue light and dark condition had slightly negative effect on seed germination.Conclusions: In comparison to blue light and dark condition, red light and white light were promoted to percentage germination indicating the role of phytochrome in seed germination of Desmodium triflorum.

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Physiological and Growth Response of Pepper (Capsicum annum L.) Seedlings to Supplementary Red/Blue Light Revealed through Transcriptomic Analysis

Agronomy ◽

10.3390/agronomy9030139 ◽

2019 ◽

Vol 9 (3) ◽

pp. 139 ◽

Cited By ~ 3

Author(s):

Zhongqi Tang ◽

Jihua Yu ◽

Jianming Xie ◽

Jian Lyu ◽

Zhi Feng ◽

...

Keyword(s):

Blue Light ◽

Differentially Expressed Genes ◽

Growth Response ◽

Enrichment Analysis ◽

Differentially Expressed ◽

Transferase Activity ◽

Full Spectrum ◽

Light Reaction ◽

Light Emitting ◽

Physiological Processes

Red and blue light have great effects on physiological processes and growth of plants. In this experiment, we investigated the physiological and growth response of pepper (Capsicum annuum L.) to supplementary red:blue (4:1) light for 1 h (T1), 3 h (T2), and 5 h (T3), and the full-spectrum light-emitting diodes, LEDs, as control (CK). Thirty-day-old seedlings were grown under these treatments for 20 days in a climate-controlled room before data measurement. The results showed that the light treatments significantly (p < 0.05) affected the photosynthesis and growth indexes as well as gene expression in the pepper seedlings. Plants under T2 generally had better performance in terms of seedling growth. A total of 124, 1283, and 1091 differentially expressed genes were found in CK vs. T1, CK vs. T2, and CK vs. T3, respectively. Among the treatments, T2 in comparison with CK had 705 upregulated and 578 downregulated differentially expressed genes (DEGs). We also found that CPRF2, Paggis, HLIPS, GIGANTEA, LSH1, and FTSH genes were expressed differently under the various light treatments. Based on GeneOntology (GO) enrichment analysis, DEGs were significantly enriched on 15 GO terms of which xyloglucan:xyloglucosyl transferase activity and apoplastic, cellular polysaccharide metabolic, and cellular carbohydrate metabolic processes were closely related to light responses. A total of 96 genes that are related to plant–pathogen interaction, zeatin biosynthesis, plant hormone signal transduction, and wax/cutin/suberine biosynthesis which are involved in the pathway of light reaction in plants were significantly enriched in T2 plants compared with plants under CK. The application of red:blue light at 4:1 for 3 h improved the growth of pepper seedlings better than the other treatments and this can be tested under the Chinese Solar Greenhouse condition.

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Transcriptome Analysis of Differentially Expressed Genes Related to the Growth and Development of the Jinghai Yellow Chicken

Genes ◽

10.3390/genes10070539 ◽

2019 ◽

Vol 10 (7) ◽

pp. 539 ◽

Cited By ~ 5

Author(s):

Fuxiang Chen ◽

Pengfei Wu ◽

Manman Shen ◽

Mingliang He ◽

Lan Chen ◽

...

Keyword(s):

Growth Rate ◽

Differentially Expressed Genes ◽

Growth And Development ◽

Slow Growth ◽

Growth Traits ◽

Fast Growth ◽

Differentially Expressed ◽

Group A ◽

Upregulated Genes ◽

Jinghai Yellow Chicken

The growth traits are important traits in chickens. Compared to white feather broiler breeds, Chinese local broiler breeds have a slow growth rate. The main genes affecting the growth traits of local chickens in China are still unclear and need to be further explored. This experiment used fast-growth and slow-growth groups of the Jinghai Yellow chicken as the research objects. Three males and three females with similar body weights were selected from the two groups at four weeks old and eight weeks old, respectively, with a total of 24 individuals selected. After slaughter, their chest muscles were taken for transcriptome sequencing. In the differentially expressed genes screening, all of the genes obtained were screened by fold change ≥ 2 and false discovery rate (FDR) < 0.05. For four-week-old chickens, a total of 172 differentially expressed genes were screened in males, where there were 68 upregulated genes and 104 downregulated genes in the fast-growth group when compared with the slow-growth group. A total of 31 differentially expressed genes were screened in females, where there were 11 upregulated genes and 20 downregulated genes in the fast-growth group when compared with the slow-growth group. For eight-week-old chickens, a total of 37 differentially expressed genes were screened in males. The fast-growth group had 28 upregulated genes and 9 downregulated genes when compared with the slow-growth group. A total of 44 differentially expressed genes were screened in females. The fast-growth group had 13 upregulated genes and 31 downregulated genes when compared with the slow-growth group. Through gene ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, many genes were found to be related to cell proliferation and differentiation, muscle growth, and cell division such as SNCG, MCL1, ARNTL, PLPPR4, VAMP1, etc. Real-time PCR results were consistent with the RNA-Seq data and validated the findings. The results of this study will help to understand the regulation mechanism of the growth and development of Jinghai Yellow chicken and provide a theoretical basis for improving the growth rate of Chinese local chicken breeds.

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Transcript profiling of neuroendocrine tumors (NETs) to identify new targets and mechanism of progression.

Journal of Clinical Oncology ◽

10.1200/jco.2019.37.4_suppl.292 ◽

2019 ◽

Vol 37 (4_suppl) ◽

pp. 292-292

Author(s):

Emily Walzer ◽

Suraj Peri ◽

Karthik Devarajan ◽

Jianming Pei ◽

Kathy Q. Cai ◽

...

Keyword(s):

Differentially Expressed Genes ◽

Transcriptome Analysis ◽

Count Data ◽

Transcriptional Repression ◽

Expression Profiles ◽

Differentially Expressed ◽

Future Research ◽

Linear Modeling ◽

M Cell ◽

Therapeutic Implications

292 Background: Few studies have characterized the molecular drivers of NET growth and mechanisms differentiating poorly differentiated (PD) and well differentiated (WD) NETs. We explored the role of dysregulated transcriptome as the principal molecular mechanism of NETs with the goal to identify novel targets and biomarkers of differentiation. Methods: With IRB approval, de-identified, formalin fixed NET samples were used to extract total RNA for transcriptome analysis. All pathology specimens were centrally reviewed. Gene expression profiles of 774 genes were obtained using nCounter platform (PanCancer pathway panel, Nanostring TechnologiesTM). The resulting count data was voom normalized and differentially expressed genes between PD and WD NETs were identified using linear modeling methods available in R-Bioconductor LIMMA package. Candidate genes with potential therapeutic implications were validated in tissue microarrays by immunohistochemistry (IHC). Results: Analysis of gene count data between 16 PD and 23 WD NETs resulted in 154 differentially expressed genes on the 774 gene panel (FDR < 10% and 2 fold change (FC) up- or down-regulated), some of which may be potential drug targets (Figure 1). E.g. Enhancer of zeste homolog 2 (EZH2), a histone methyltransferase responsible for transcriptional repression, and CHK1, a G2/M cell cycle regulator, were upregulated in PD compared to WD NETs (2.7 and 3.1 FC, respectively) and serine/threonine-protein kinase PAK 3, involved in cytoskeleton reorganization, was upregulated in WD NETs (3.4 FC). IHC staining also suggested overexpression of EZH2 and its enzymatic substrate H3K27me in PD NETs (p < 0.001). PAK 3, another novel therapeutic candidate overexpressed in WD NETs (p < 0.001) was confirmed using IHC, validating the transcriptome analysis at protein level. Conclusions: These findings, combined with previously reported pathway analysis (Vijayvergia et.al 2017)], highlight biological differences between PD and WD NETs and serve as a platform for future research. They also support investigation of novel drugs that inhibit activity of EZH2 (e.g. EPZ6438) in PD NETs and PAK3 (e.g FRAX597) in WD NETs.

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The Effects of Red Versus Blue Lights and Neuroticism on Voluntary Biceps Brachii Muscle Contraction

Perceptual and Motor Skills ◽

10.1177/0031512518821786 ◽

2019 ◽

Vol 126 (2) ◽

pp. 253-266

Author(s):

Erdal Binboğa ◽

Serdar Tok ◽

Mustafa Munzuroğlu ◽

Aykut Eren Canüzmez ◽

Nihal Dal

Keyword(s):

Blue Light ◽

Biceps Brachii ◽

Red Light ◽

Light Condition ◽

Elbow Flexion ◽

Voluntary Contraction ◽

Biceps Brachii Muscle ◽

Personality Differences ◽

Individual Personality ◽

Median Split

This study investigated the effects of red and blue monochromatic lights and neuroticism on athletes’ maximal isometric voluntary contraction (iMVC) level of the biceps brachii muscle. During elbow flexion, we measured iMVCs under a white light (control) condition and under red and blue light conditions. Under red light (vs. white and blue), participants demonstrated a greater iMVC level. Further, based on a median split of the athletes’ scores on Tatar’s Five Factor Personality Inventory, high and low neuroticism groups showed no red light differences, while, in the blue light condition, participants high in neuroticism increased the iMVC level by 4.04% and those low in neuroticism decreased iMVC level by 6.31%. Thus, the effect of colored light on athletes’ motor output varied with individual personality differences in neuroticism.

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The Physiological Response of Lettuce to Red and Blue Light Dynamics Over Different Photoperiods

Frontiers in Plant Science ◽

10.3389/fpls.2020.610174 ◽

2021 ◽

Vol 11 ◽

Author(s):

Giedrė Samuolienė ◽

Akvilė Viršilė ◽

Jurga Miliauskienė ◽

Perttu J. Haimi ◽

Kristina Laužikė ◽

...

Keyword(s):

Blue Light ◽

Physiological Response ◽

Nutritive Value ◽

Leaf Gas Exchange ◽

Soluble Sugar ◽

Soluble Sugars ◽

Red Light ◽

Antioxidant Properties ◽

Photon Flux ◽

Light Spectrum

This study aimed to evaluate the effect of dynamic red and blue light parameters on the physiological responses and key metabolites in lettuce and also the subsequent impact of varying light spectra on nutritive value. We explored the metabolic changes in carotenes, xanthophylls, soluble sugars, organic acids, and antioxidants; the response of photosynthetic indices [photosynthetic (Pr) and transpiration (Tr) rates]; and the intracellular to ambient CO2 concentration ratios (Ci/Ca) in lettuce (Lactuca sativa L. “Lobjoits Green Cos”). They were cultivated under constant (con) or parabolic (dyn) blue (B, 452 nm) and/or red (R, 662 nm) light-emitting diode (LED) photosynthetic photon flux densities (PPFDs) at 12, 16, and 20 h photoperiods, maintaining consistent daily light integrals (DLIs) for each light component in all treatments, at 2.3 and 9.2 mol m–2 per day for blue and red light, respectively. The obtained results and principal component analysis (PCA) confirmed a significant impact of the light spectrum, photoperiod, and parabolic profiles of PPFD on the physiological response of lettuce. The 16 h photoperiod resulted in significantly higher content of xanthophylls (neoxanthin, violaxanthin, lutein, and zeaxanthin) in lettuce leaves under both constant and parabolic blue light treatments (BconRdyn 16 h and BdynRdyn 16 h, respectively). Lower PPFD levels under a 20 h photoperiod (BdynRdyn 20 h) as well as higher PPFD levels under a 12 h photoperiod (BdynRdyn 12 h) had a pronounced impact on leaf gas exchange indices (Pr, Tr, Ci/Ca), xanthophylls, soluble sugar contents, and antioxidant properties of lettuce leaves. The parabolic PPFD lighting profile over a 16 h photoperiod (BdynRdyn 16 h) led to a significant decrease in Ci/Ca, which resulted in decreased Pr and Tr, compared with constant blue or red light treatments with the same photoperiod (BconRdyn and BdynRcon 16 h). Additionally, constant blue lighting produced higher α + β-carotene and anthocyanin (ARI) content and increased carotenoid to chlorophyll ratio (CRI) but decreased biomass accumulation and antioxidant activity.

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Transcriptomics analysis reveals the signal transduction mechanism of brassinolides in tea leaves and its regulation on the growth and development of Camellia sinensis

BMC Genomics ◽

10.1186/s12864-021-08179-9 ◽

2022 ◽

Vol 23 (1) ◽

Author(s):

Qifang Jin ◽

Zhong Wang ◽

Yanni Chen ◽

Yiping Luo ◽

Na Tian ◽

...

Keyword(s):

Signal Transduction ◽

Differentially Expressed Genes ◽

Camellia Sinensis ◽

Growth And Development ◽

Cell Structure ◽

Enrichment Analysis ◽

Differentially Expressed ◽

Pathway Enrichment Analysis ◽

Tea Leaves ◽

Depth Analysis

Abstract Background Brassinosteroids (BRs) are a type of sterol plant hormone that play an important role in various biochemical and physiological reactions such as promoting cell growth, increasing biomass, and improving stress resistance. Results To investigate the regulatory and molecular mechanism of BRs on the growth and development of tea plants (Camellia sinensis L.), changes in cell structure and gene expression levels of tea leaves treated with exogenous BRs were analyzed by electron microscopy and high-throughput Illumina RNA-Seq technology. The results showed that the number of starch granules in the chloroplasts and lipid globules increased and thylakoids expanded after BR treatment compared with the control. Transcriptome analysis showed that in the four BR treatments (CAA: BR treatment for 3 h, CAB: BR treatment for 9 h, CAC: BR treatment for 24 h, and CAD: BR treatment for 48 h), 3861 (1867 upregulated and 1994 downregulated), 5030 (2461 upregulated and 2569 downregulated), 1626 (815 upregulated and 811 downregulated), and 2050 (1004 upregulated and 1046 downregulated) differentially expressed genes were detected, respectively, compared with CAK (BR treatment for 0 h). Using Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, metabolic pathway enrichment analysis showed that the differentially expressed genes of CAA vs. CAK, CAB vs. CAK, CAC vs. CAK, and CAD vs. CAK significantly enriched the functional categories of signal transduction, cell cycle regulation, and starch, sucrose, and flavonoid biosynthesis and metabolism pathways. We also found that after spraying BR, the key genes for caffeine synthesis were downregulated. The results of qRT-PCR coincided with the findings of transcriptomic analysis. Conclusions The present study improved our understanding of the effects of BRs on the growth and development of tea leaves and laid the foundation for the in-depth analysis of signal transduction pathways of BRs in tea leaves.

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